java.lang.Object
- htsjdk.samtools.SAMRecord
- - htsjdk.samtools.sra.SRALazyRecord

All Implemented Interfaces:

Locatable, Serializable, Cloneable
```
public class SRALazyRecord
extends SAMRecord
```
Extends SAMRecord so that any of the fields will be loaded only when needed. Since SRA is a column oriented database, it is very inefficient to load all the fields at once. However, loading only set of actually needed fields will be even faster than in row oriented databases. Because of that we are providing lazy loading of fields, flags and attributes. Created by andrii.nikitiuk on 8/25/15.

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class htsjdk.samtools.SAMRecord
  SAMRecord.SAMTagAndValue

Field Summary
- Fields inherited from class htsjdk.samtools.SAMRecord
  MAX_INSERT_SIZE, mMateReferenceIndex, mReferenceIndex, NO_ALIGNMENT_CIGAR, NO_ALIGNMENT_REFERENCE_INDEX, NO_ALIGNMENT_REFERENCE_NAME, NO_ALIGNMENT_START, NO_MAPPING_QUALITY, NULL_QUALS, NULL_QUALS_STRING, NULL_SEQUENCE, NULL_SEQUENCE_STRING, serialVersionUID, TAGS_TO_REVERSE, TAGS_TO_REVERSE_COMPLEMENT, UNKNOWN_MAPPING_QUALITY

Constructor Summary

Constructors
Modifier	Constructor	Description
`protected`	`SRALazyRecord(SAMFileHeader header, SRAAccession accession, String readId, int unalignedReadFragmentIndex)`
`protected`	`SRALazyRecord(SAMFileHeader header, SRAAccession accession, String readId, String alignmentId)`
	`SRALazyRecord(SAMFileHeader header, SRAAccession accession, ngs.ReadCollection run, ngs.AlignmentIterator alignmentIterator, String readId, String alignmentId)`
	`SRALazyRecord(SAMFileHeader header, SRAAccession accession, ngs.ReadCollection run, ngs.ReadIterator unalignmentIterator, String readId, int unalignedReadFragmentIndex)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`clearAttributes()`	Removes all attributes.
`Object`	`clone()`	Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator
`void`	`detachFromIterator()`	Is being called when original NGS iterator is being moved to the next object.
`boolean`	`equals(Object o)`	For records equality, we should only compare read id, reference and position on the reference.
`String`	`format()`
`int`	`getAlignmentStart()`
`Object`	`getAttribute(short tag)`
`byte[]`	`getBaseQualities()`	Do not modify the value returned by this method.
`protected SAMBinaryTagAndValue`	`getBinaryAttributes()`
`Cigar`	`getCigar()`	Do not modify the value returned by this method.
`String`	`getCigarString()`
`boolean`	`getFirstOfPairFlag()`	the read is the first read in a pair.
`int`	`getFlags()`	It is preferable to use the get*Flag() methods that handle the flag word symbolically.
`int`	`getInferredInsertSize()`
`int`	`getMappingQuality()`
`int`	`getMateAlignmentStart()`
`boolean`	`getMateNegativeStrandFlag()`	strand of the mate (false for forward; true for reverse strand).
`Integer`	`getMateReferenceIndex()`	Returns the mate reference index for this record.
`String`	`getMateReferenceName()`
`boolean`	`getMateUnmappedFlag()`	the mate is unmapped.
`boolean`	`getProperPairFlag()`	the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
`byte[]`	`getReadBases()`	Do not modify the value returned by this method.
`boolean`	`getReadNegativeStrandFlag()`	strand of the query (false for forward; true for reverse strand).
`boolean`	`getReadPairedFlag()`	the read is paired in sequencing, no matter whether it is mapped in a pair.
`Integer`	`getReferenceIndex()`	Returns the reference index for this record.
`String`	`getReferenceName()`
`boolean`	`getSecondOfPairFlag()`	the read is the second read in a pair.
`int`	`hashCode()`	The same approach as with 'equals' method.
`boolean`	`isSecondaryAlignment()`
`boolean`	`isUnsignedArrayAttribute(String tag)`
`List<SAMValidationError>`	`isValid(boolean firstOnly)`	Perform various validations of SAMRecord.
`void`	`setAlignmentStart(int value)`
`void`	`setAttribute(short tag, Object value)`
`protected void`	`setAttribute(short tag, Object value, boolean isUnsignedArray)`
`protected void`	`setAttributes(SAMBinaryTagAndValue attributes)`	Replace any existing attributes with the given linked item.
`void`	`setBaseQualities(byte[] value)`
`void`	`setCigar(Cigar value)`	For setting the Cigar string when changed.
`void`	`setCigarString(String value)`
`void`	`setFirstOfPairFlag(boolean flag)`	the read is the first read in a pair.
`void`	`setFlags(int value)`
`void`	`setInferredInsertSize(int value)`
`void`	`setMappingQuality(int value)`
`void`	`setMateAlignmentStart(int value)`
`void`	`setMateNegativeStrandFlag(boolean flag)`	strand of the mate (false for forward; true for reverse strand).
`void`	`setMateReferenceIndex(int value)`	Updates the mate reference index.
`void`	`setMateReferenceName(String value)`	Sets the mate reference name for this record.
`void`	`setMateUnmappedFlag(boolean flag)`	the mate is unmapped.
`void`	`setProperPairFlag(boolean flag)`	the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
`void`	`setReadBases(byte[] value)`
`void`	`setReadNegativeStrandFlag(boolean flag)`	strand of the query (false for forward; true for reverse strand).
`void`	`setReadPairedFlag(boolean flag)`	the read is paired in sequencing, no matter whether it is mapped in a pair.
`void`	`setReferenceIndex(int value)`	Updates the reference index.
`void`	`setReferenceName(String value)`	Sets the reference name for this record.
`void`	`setSecondaryAlignment(boolean flag)`	set whether this alignment is secondary (an alternative alignment of the read).
`void`	`setSecondOfPairFlag(boolean flag)`	the read is the second read in a pair.

Methods inherited from class htsjdk.samtools.SAMRecord
computeIndexingBinIfAbsent, deepCopy, eagerDecode, getAlignmentBlocks, getAlignmentEnd, getAttribute, getAttributes, getAttributesBinarySize, getBaseQualityString, getByteArrayAttribute, getByteAttribute, getCharacterAttribute, getCigarLength, getContig, getDuplicateReadFlag, getEnd, getFileSource, getFloatArrayAttribute, getFloatAttribute, getHeader, getIntegerAttribute, getNotPrimaryAlignmentFlag, getOriginalBaseQualities, getPairedReadName, getReadFailsVendorQualityCheckFlag, getReadGroup, getReadLength, getReadName, getReadNameLength, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadPositionAtReferencePosition, getReadString, getReadUnmappedFlag, getReferencePositionAtReadPosition, getReferencePositionAtReadPosition, getSAMFlags, getSAMString, getShortAttribute, getSignedByteArrayAttribute, getSignedIntArrayAttribute, getSignedShortArrayAttribute, getStart, getStringAttribute, getSupplementaryAlignmentFlag, getTransientAttribute, getUnclippedEnd, getUnclippedStart, getUnsignedByteArrayAttribute, getUnsignedIntArrayAttribute, getUnsignedIntegerAttribute, getUnsignedIntegerAttribute, getUnsignedShortArrayAttribute, getValidationStringency, getVariableBinaryRepresentation, hasAttribute, initializeCigar, isAllowedAttributeValue, isSecondaryOrSupplementary, isValid, removeTransientAttribute, resolveIndexFromName, resolveNameFromIndex, reverseComplement, reverseComplement, reverseComplement, setAttribute, setBaseQualityString, setDuplicateReadFlag, setFileSource, setHeader, setHeaderStrict, setNotPrimaryAlignmentFlag, setOriginalBaseQualities, setReadFailsVendorQualityCheckFlag, setReadName, setReadString, setReadUmappedFlag, setReadUnmappedFlag, setSupplementaryAlignmentFlag, setTransientAttribute, setUnsignedArrayAttribute, setValidationStringency, toString, validateCigar

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

- Constructor Detail
  - SRALazyRecord
```
public SRALazyRecord(SAMFileHeader header,
                     SRAAccession accession,
                     ngs.ReadCollection run,
                     ngs.AlignmentIterator alignmentIterator,
                     String readId,
                     String alignmentId)
```
  - SRALazyRecord
```
public SRALazyRecord(SAMFileHeader header,
                     SRAAccession accession,
                     ngs.ReadCollection run,
                     ngs.ReadIterator unalignmentIterator,
                     String readId,
                     int unalignedReadFragmentIndex)
```
  - SRALazyRecord
```
protected SRALazyRecord(SAMFileHeader header,
                        SRAAccession accession,
                        String readId,
                        String alignmentId)
```
  - SRALazyRecord
```
protected SRALazyRecord(SAMFileHeader header,
                        SRAAccession accession,
                        String readId,
                        int unalignedReadFragmentIndex)
```
- Method Detail
  - detachFromIterator
```
public void detachFromIterator()
```
    Is being called when original NGS iterator is being moved to the next object. Later, if any of uninitialized fields is requested, either Read object or Alignment has to be retrieved from ReadCollection
  - getAlignmentStart
```
public int getAlignmentStart()
```
    Overrides:
    
    getAlignmentStart in class SAMRecord
    
    Returns:
    
    1-based inclusive leftmost position of the sequence remaining after clipping, or 0 if there is no position, e.g. for unmapped read.
  - setAlignmentStart
```
public void setAlignmentStart(int value)
```
    Overrides:
    
    setAlignmentStart in class SAMRecord
    
    Parameters:
    
    value - 1-based inclusive leftmost position of the sequence remaining after clipping or 0 if there is no position, e.g. for unmapped read.
  - getMappingQuality
```
public int getMappingQuality()
```
    Overrides:
    
    getMappingQuality in class SAMRecord
    
    Returns:
    
    phred scaled mapping quality. 255 implies valid mapping but quality is hard to compute.
  - setMappingQuality
```
public void setMappingQuality(int value)
```
    Overrides:
    
    setMappingQuality in class SAMRecord
  - getReferenceName
```
public String getReferenceName()
```
    Overrides:
    
    getReferenceName in class SAMRecord
    
    Returns:
    
    Reference name, or NO_ALIGNMENT_REFERENCE_NAME (*) if the record has no reference name
  - setReferenceName
```
public void setReferenceName(String value)
```
    Description copied from class: SAMRecord
    
    Sets the reference name for this record. If the record has a valid SAMFileHeader and the reference name is present in the associated sequence dictionary, the record's reference index will also be updated with the corresponding sequence index. If referenceName is NO_ALIGNMENT_REFERENCE_NAME, sets the reference index to NO_ALIGNMENT_REFERENCE_INDEX.
    
    Overrides:
    
    setReferenceName in class SAMRecord
    
    Parameters:
    
    value - - must not be null
  - getReferenceIndex
```
public Integer getReferenceIndex()
```
    Description copied from class: SAMRecord
    
    Returns the reference index for this record. If the reference name for this record has previously been resolved against the sequence dictionary, the corresponding index is returned directly. Otherwise, the record must have a non-null SAMFileHeader that can be used to resolve the index for the record's current reference name, unless the reference name is NO_ALIGNMENT_REFERENCE_NAME. If the record has a header, and the name does not appear in the header's sequence dictionary, the value NO_ALIGNMENT_REFERENCE_INDEX (-1) will be returned. If the record does not have a header, an IllegalStateException is thrown.
    
    Overrides:
    
    getReferenceIndex in class SAMRecord
    
    Returns:
    
    Index in the sequence dictionary of the reference sequence. If the read has no reference sequence, or if the reference name is not found in the sequence index, NO_ALIGNMENT_REFERENCE_INDEX (-1) is returned.
  - setReferenceIndex
```
public void setReferenceIndex(int value)
```
    Description copied from class: SAMRecord
    
    Updates the reference index. The record must have a valid SAMFileHeader unless the referenceIndex parameter equals NO_ALIGNMENT_REFERENCE_INDEX, and the reference index must appear in the header's sequence dictionary. If the reference index is valid, the reference name will also be resolved and updated to the name for the sequence dictionary entry corresponding to the index.
    
    Overrides:
    
    setReferenceIndex in class SAMRecord
    
    Parameters:
    
    value - Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the record must have a SAMFileHeader and the index must exist in the associated sequence dictionary.
  - getCigarString
```
public String getCigarString()
```
    Overrides:
    
    getCigarString in class SAMRecord
  - setCigarString
```
public void setCigarString(String value)
```
    Overrides:
    
    setCigarString in class SAMRecord
  - getCigar
```
public Cigar getCigar()
```
    Description copied from class: SAMRecord
    
    Do not modify the value returned by this method. If you want to change the Cigar, create a new Cigar and call setCigar() or call setCigarString()
    
    Overrides:
    
    getCigar in class SAMRecord
    
    Returns:
    
    Cigar object for the read, or null if there is none.
  - setCigar
```
public void setCigar(Cigar value)
```
    Description copied from class: SAMRecord
    
    For setting the Cigar string when changed. Note that this nulls the indexing bin, which would need to be recomputed on write (if needed). To avoid clobbering the indexing bin, use SAMRecord.initializeCigar(htsjdk.samtools.Cigar)
    
    Overrides:
    
    setCigar in class SAMRecord
  - getReadBases
```
public byte[] getReadBases()
```
    Description copied from class: SAMRecord
    
    Do not modify the value returned by this method. If you want to change the bases, create a new byte[] and call setReadBases() or call setReadString().
    
    Overrides:
    
    getReadBases in class SAMRecord
    
    Returns:
    
    read sequence as ASCII bytes ACGTN=.
  - setReadBases
```
public void setReadBases(byte[] value)
```
    Overrides:
    
    setReadBases in class SAMRecord
  - getBaseQualities
```
public byte[] getBaseQualities()
```
    Description copied from class: SAMRecord
    
    Do not modify the value returned by this method. If you want to change the qualities, create a new byte[] and call setBaseQualities() or call setBaseQualityString().
    
    Overrides:
    
    getBaseQualities in class SAMRecord
    
    Returns:
    
    Base qualities, as binary phred scores (not ASCII).
  - setBaseQualities
```
public void setBaseQualities(byte[] value)
```
    Overrides:
    
    setBaseQualities in class SAMRecord
  - getMateAlignmentStart
```
public int getMateAlignmentStart()
```
    Overrides:
    
    getMateAlignmentStart in class SAMRecord
    
    Returns:
    
    1-based inclusive leftmost position of the clipped mate sequence, or 0 if there is no position.
  - setMateAlignmentStart
```
public void setMateAlignmentStart(int value)
```
    Overrides:
    
    setMateAlignmentStart in class SAMRecord
  - getMateReferenceName
```
public String getMateReferenceName()
```
    Overrides:
    
    getMateReferenceName in class SAMRecord
    
    Returns:
    
    Mate reference name, or NO_ALIGNMENT_REFERENCE_NAME (*) if the record has no mate reference name
  - setMateReferenceName
```
public void setMateReferenceName(String value)
```
    Description copied from class: SAMRecord
    
    Sets the mate reference name for this record. If the record has a valid SAMFileHeader and the mate reference name is present in the associated sequence dictionary, the record's mate reference index will also be updated with the corresponding sequence index. If mateReferenceName is NO_ALIGNMENT_REFERENCE_NAME, sets the mate reference index to NO_ALIGNMENT_REFERENCE_INDEX.
    
    Overrides:
    
    setMateReferenceName in class SAMRecord
    
    Parameters:
    
    value - - must not be null
  - getMateReferenceIndex
```
public Integer getMateReferenceIndex()
```
    Description copied from class: SAMRecord
    
    Returns the mate reference index for this record. If the mate reference name for this record has previously been resolved against the sequence dictionary, the corresponding index is returned directly. Otherwise, the record must have a non-null SAMFileHeader that can be used to resolve the index for the record's current mate reference name, unless the mate reference name is NO_ALIGNMENT_REFERENCE_NAME. If the record has a header, and the name does not appear in the header's sequence dictionary, the value NO_ALIGNMENT_REFERENCE_INDEX (-1) will be returned. If the record does not have a header, an IllegalStateException is thrown.
    
    Overrides:
    
    getMateReferenceIndex in class SAMRecord
    
    Returns:
    
    Index in the sequence dictionary of the mate reference sequence. If the read has no mate reference sequence, or if the mate reference name is not found in the sequence index, NO_ALIGNMENT_REFERENCE_INDEX (-1) is returned.
  - setMateReferenceIndex
```
public void setMateReferenceIndex(int value)
```
    Description copied from class: SAMRecord
    
    Updates the mate reference index. The record must have a valid SAMFileHeader, and the mate reference index must appear in the header's sequence dictionary, unless the mateReferenceIndex parameter equals NO_ALIGNMENT_REFERENCE_INDEX. If the mate reference index is valid, the mate reference name will also be resolved and updated to the name for the sequence dictionary entry corresponding to the index.
    
    Overrides:
    
    setMateReferenceIndex in class SAMRecord
    
    Parameters:
    
    value - Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the record must have a SAMFileHeader and the index must exist in the associated sequence dictionary.
  - getInferredInsertSize
```
public int getInferredInsertSize()
```
    Overrides:
    
    getInferredInsertSize in class SAMRecord
    
    Returns:
    
    insert size (difference btw 5' end of read & 5' end of mate), if possible, else 0. Negative if mate maps to lower position than read.
  - setInferredInsertSize
```
public void setInferredInsertSize(int value)
```
    Overrides:
    
    setInferredInsertSize in class SAMRecord
  - getFlags
```
public int getFlags()
```
    Description copied from class: SAMRecord
    
    It is preferable to use the get*Flag() methods that handle the flag word symbolically.
    
    Overrides:
    
    getFlags in class SAMRecord
  - setFlags
```
public void setFlags(int value)
```
    Overrides:
    
    setFlags in class SAMRecord
  - getReadNegativeStrandFlag
```
public boolean getReadNegativeStrandFlag()
```
    Description copied from class: SAMRecord
    
    strand of the query (false for forward; true for reverse strand).
    
    Overrides:
    
    getReadNegativeStrandFlag in class SAMRecord
  - setReadNegativeStrandFlag
```
public void setReadNegativeStrandFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    strand of the query (false for forward; true for reverse strand).
    
    Overrides:
    
    setReadNegativeStrandFlag in class SAMRecord
  - getReadPairedFlag
```
public boolean getReadPairedFlag()
```
    Description copied from class: SAMRecord
    
    the read is paired in sequencing, no matter whether it is mapped in a pair.
    
    Overrides:
    
    getReadPairedFlag in class SAMRecord
  - setReadPairedFlag
```
public void setReadPairedFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    the read is paired in sequencing, no matter whether it is mapped in a pair.
    
    Overrides:
    
    setReadPairedFlag in class SAMRecord
  - getProperPairFlag
```
public boolean getProperPairFlag()
```
    Description copied from class: SAMRecord
    
    the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
    
    Overrides:
    
    getProperPairFlag in class SAMRecord
  - setProperPairFlag
```
public void setProperPairFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
    
    Overrides:
    
    setProperPairFlag in class SAMRecord
  - isSecondaryAlignment
```
public boolean isSecondaryAlignment()
```
    Overrides:
    
    isSecondaryAlignment in class SAMRecord
    
    Returns:
    
    whether the alignment is secondary (an alternative alignment of the read).
  - setSecondaryAlignment
```
public void setSecondaryAlignment(boolean flag)
```
    Description copied from class: SAMRecord
    
    set whether this alignment is secondary (an alternative alignment of the read).
    
    Overrides:
    
    setSecondaryAlignment in class SAMRecord
  - getMateNegativeStrandFlag
```
public boolean getMateNegativeStrandFlag()
```
    Description copied from class: SAMRecord
    
    strand of the mate (false for forward; true for reverse strand).
    
    Overrides:
    
    getMateNegativeStrandFlag in class SAMRecord
  - setMateNegativeStrandFlag
```
public void setMateNegativeStrandFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    strand of the mate (false for forward; true for reverse strand).
    
    Overrides:
    
    setMateNegativeStrandFlag in class SAMRecord
  - getMateUnmappedFlag
```
public boolean getMateUnmappedFlag()
```
    Description copied from class: SAMRecord
    
    the mate is unmapped.
    
    Overrides:
    
    getMateUnmappedFlag in class SAMRecord
  - setMateUnmappedFlag
```
public void setMateUnmappedFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    the mate is unmapped.
    
    Overrides:
    
    setMateUnmappedFlag in class SAMRecord
  - getFirstOfPairFlag
```
public boolean getFirstOfPairFlag()
```
    Description copied from class: SAMRecord
    
    the read is the first read in a pair.
    
    Overrides:
    
    getFirstOfPairFlag in class SAMRecord
  - setFirstOfPairFlag
```
public void setFirstOfPairFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    the read is the first read in a pair.
    
    Overrides:
    
    setFirstOfPairFlag in class SAMRecord
  - getSecondOfPairFlag
```
public boolean getSecondOfPairFlag()
```
    Description copied from class: SAMRecord
    
    the read is the second read in a pair.
    
    Overrides:
    
    getSecondOfPairFlag in class SAMRecord
  - setSecondOfPairFlag
```
public void setSecondOfPairFlag(boolean flag)
```
    Description copied from class: SAMRecord
    
    the read is the second read in a pair.
    
    Overrides:
    
    setSecondOfPairFlag in class SAMRecord
  - getAttribute
```
public Object getAttribute(short tag)
```
    Overrides:
    
    getAttribute in class SAMRecord
    
    Parameters:
    
    tag - Binary representation of a 2-char String tag as created by SAMTagUtil.
    
    See Also:
    
    SAMRecord.getAttribute(java.lang.String)
  - setAttribute
```
public void setAttribute(short tag,
                         Object value)
```
    Overrides:
    
    setAttribute in class SAMRecord
    
    Parameters:
    
    tag - Binary representation of a 2-char String tag as created by SAMTagUtil.
    
    See Also:
    
    SAMRecord.setAttribute(java.lang.String, java.lang.Object)
  - setAttribute
```
protected void setAttribute(short tag,
                            Object value,
                            boolean isUnsignedArray)
```
    Overrides:
    
    setAttribute in class SAMRecord
  - clearAttributes
```
public void clearAttributes()
```
    Description copied from class: SAMRecord
    
    Removes all attributes.
    
    Overrides:
    
    clearAttributes in class SAMRecord
  - setAttributes
```
protected void setAttributes(SAMBinaryTagAndValue attributes)
```
    Description copied from class: SAMRecord
    
    Replace any existing attributes with the given linked item. NOTE: this method is intended to only be called from subclasses.
    
    Overrides:
    
    setAttributes in class SAMRecord
  - getBinaryAttributes
```
protected SAMBinaryTagAndValue getBinaryAttributes()
```
    Overrides:
    
    getBinaryAttributes in class SAMRecord
    
    Returns:
    
    Pointer to the first of the tags. Returns null if there are no tags.
  - isUnsignedArrayAttribute
```
public boolean isUnsignedArrayAttribute(String tag)
```
    Overrides:
    
    isUnsignedArrayAttribute in class SAMRecord
    
    Returns:
    
    True if this tag is an unsigned array, else false.
  - equals
```
public boolean equals(Object o)
```
    For records equality, we should only compare read id, reference and position on the reference. Since read id is a constructor parameter, we only need to make sure that reference info is loaded.
    
    Overrides:
    
    equals in class SAMRecord
    
    Parameters:
    
    o - other
    
    Returns:
    
    comparison result
  - hashCode
```
public int hashCode()
```
    The same approach as with 'equals' method. We only load reference and position.
    
    Overrides:
    
    hashCode in class SAMRecord
  - clone
```
public Object clone()
             throws CloneNotSupportedException
```
    Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator
    
    Overrides:
    
    clone in class SAMRecord
    
    Returns:
    
    new object
    
    Throws:
    
    CloneNotSupportedException
  - format
```
public String format()
```
    Overrides:
    
    format in class SAMRecord
    
    Returns:
    
    String representation of this.
  - isValid
```
public List<SAMValidationError> isValid(boolean firstOnly)
```
    Description copied from class: SAMRecord
    
    Perform various validations of SAMRecord. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable. A record with null a header may be validated by the isValid method, but the reference and mate reference indices, read group, sequence dictionary, and alignment start will not be fully validated unless a header is present.
    
    Overrides:
    
    isValid in class SAMRecord
    
    Parameters:
    
    firstOnly - return only the first error if true, false otherwise
    
    Returns:
    
    null if valid. If invalid, returns a list of error messages.

Class SRALazyRecord

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.samtools.SAMRecord

Field Summary

Fields inherited from class htsjdk.samtools.SAMRecord

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.SAMRecord

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.util.Locatable

Constructor Detail

SRALazyRecord

SRALazyRecord

SRALazyRecord

SRALazyRecord

Method Detail

detachFromIterator

getAlignmentStart

setAlignmentStart

getMappingQuality

setMappingQuality

getReferenceName

setReferenceName

getReferenceIndex

setReferenceIndex

getCigarString

setCigarString

getCigar

setCigar

getReadBases

setReadBases

getBaseQualities

setBaseQualities

getMateAlignmentStart

setMateAlignmentStart

getMateReferenceName

setMateReferenceName

getMateReferenceIndex

setMateReferenceIndex

getInferredInsertSize

setInferredInsertSize

getFlags

setFlags

getReadNegativeStrandFlag

setReadNegativeStrandFlag

getReadPairedFlag

setReadPairedFlag

getProperPairFlag

setProperPairFlag

isSecondaryAlignment

setSecondaryAlignment

getMateNegativeStrandFlag

setMateNegativeStrandFlag

getMateUnmappedFlag

setMateUnmappedFlag

getFirstOfPairFlag

setFirstOfPairFlag

getSecondOfPairFlag

setSecondOfPairFlag

getAttribute

setAttribute

setAttribute

clearAttributes

setAttributes

getBinaryAttributes

isUnsignedArrayAttribute

equals

hashCode

clone

format

isValid